Abstract
Plant-specific fasciclin-like arabinogalactan proteins (FLAs) are a subclass of the arabinogalactan proteins (AGPs) superfamily. In addition to AGP-like glycosylated regions, FLAs have conserved fasciclin (FAS) domains. Here, we identified 220 FLA genes from seven Rosaceae species, including 38 FLA gene in pear. Based on gene structure and phylogenetic analysis, the Rosaceae FLA genes can be divided into four classes. The Ks and 4DTv values suggested that the PbrFLA gene family had undergone two whole-genome duplication events occurring at 30–45 MYA and ~ 140 MYA, respectively. Whole-genome duplication (WGD) and transposed duplication (TRD) events mainly drove the evolution of PbrFLA gene family. Most pear FLAs from pear had no intron in their genomic DNA sequences. Pear FLAs possess two highly conserved regions (H1 and H2) and the conserved [Tyr Phe] His ([Y/F]H) motif locating between these two regions. Based on gene expression analysis, most pear FLAs exhibited tissue-specific patterns. PbrFLA10, PbrFLA20, and PbrFLA21 were highly expressed in pollen tubes and self-pollinated styles, indicating FLAs play roles in pollen tube growth and self-incompatibility response. Repression of PbrFLA10/20/21 resulted in the acceleration of pear pollen tube growth. Taken together, our results provided information for understanding the evolution of the PbrFLA gene family and identified the key PbrFLAs genes regulating pollen tube growth.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Availability of data and materials
All coding and protein sequences in this study can be found in the Genome Database for Rosaceae (https://www.rosaceae.org/) and Pear Genome Project (http://peargenome.njau.edu.cn/).
References
Blanc G, Wolfe KH (2004) Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Pl Cell 16:1667–1678. https://doi.org/10.1105/tpc.021345
Castilleux R, Plancot B, Ropitaux M, Carreras A, Leprince J, Boulogne I, Follet-Gueye ML, Popper ZA, Driouich A, Vicre M (2018) Cell wall extensins in root-microbe interactions and root secretions. J Exp Bot 69:4235–4247. https://doi.org/10.1093/jxb/ery238
Chen J, Li X, Wang D, Li L, Zhou H, Liu Z, Wu J, Wang P, Jiang X, Fabrice MR, Zhang S, Wu J (2015) Identification and testing of reference genes for gene expression analysis in pollen of Pyrus bretschneideri. Sci Hort 190:43–56. https://doi.org/10.1016/j.scienta.2015.04.010
Chen J, Wang P, de Graaf BHJ, Zhang H, Jiao H, Tang C, Zhang S, Wu J (2018a) Phosphatidic acid counteracts S-RNase signaling in pollen by stabilizing the actin cytoskeleton. Pl Cell 30:1023–1039. https://doi.org/10.1105/tpc.18.00021
Chen S, Zhou Y, Chen Y, Gu J (2018b) fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34:i884–i890. https://doi.org/10.1093/bioinformatics/bty560
Chen C, Chen H, Zhang Y, Thomas HR, Frank MH, He Y, Xia R (2020) TBtools: an integrative toolkit developed for interactive analyses of big biological data. Mol Pl 13:1194–1202. https://doi.org/10.1016/j.molp.2020.06.009
Coimbra S, Costa M, Jones B, Mendes MA, Pereira LG (2009) Pollen grain development is compromised in Arabidopsis agp6 agp11 null mutants. J Exp Bot 60:3133–3142. https://doi.org/10.1093/jxb/erp148
Costa M, Pereira AM, Pinto SC, Silva J, Pereira LG, Coimbra S (2019) In silico and expression analyses of fasciclin-like arabinogalactan proteins reveal functional conservation during embryo and seed development. Pl Reprod 32:353–370. https://doi.org/10.1007/s00497-019-00376-7
Cruz-Garcia F, Nathan Hancock C, Kim D, McClure B (2005) Stylar glycoproteins bind to S-RNase in vitro. Pl J 42:295–304. https://doi.org/10.1111/j.1365-313X.2005.02375.x
Eddy SR (2011) Accelerated profile HMM searches. PLoS Comput Biol 7:e1002195. https://doi.org/10.1371/journal.pcbi.1002195
Eisenhaber B, Bork P, Eisenhaber F (1999) Prediction of potential GPI-modification sites in proprotein sequences. J Molec Biol 292:741–758. https://doi.org/10.1006/jmbi.1999.3069
Faik A, Abouzouhair J, Sarhan F (2006) Putative fasciclin-like arabinogalactan-proteins (FLA) in wheat (Triticum aestivum) and rice (Oryza sativa): identification and bioinformatic analyses. Molec Genet Genomics 276:478–494. https://doi.org/10.1007/s00438-006-0159-z
Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, Holm L, Sonnhammer EL, Eddy SR, Bateman A (2010) The Pfam protein families database. Nucl Acids Res 38:D211-222. https://doi.org/10.1093/nar/gkp985
Guerriero G, Mangeot-Peter L, Legay S, Behr M, Lutts S, Siddiqui KS, Hausman JF (2017) Identification of fasciclin-like arabinogalactan proteins in textile hemp (Cannabis sativa L.): in silico analyses and gene expression patterns in different tissues. BMC Genom 18:741. https://doi.org/10.1186/s12864-017-3970-5
Han YY, Zhou HY, Xu LA, Liu XY, Fan SX, Cao JS (2018) The zinc-finger transcription factor BcMF20 and its orthologs in Cruciferae which are required for pollen development. Biochem Biophys Res Commun 503:998–1003. https://doi.org/10.1016/j.bbrc.2018.06.108
Hasegawa M, Kishino H, Yano T (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Molec Evol 22:160–174. https://doi.org/10.1007/BF02101694
He J, Zhao H, Cheng Z, Ke Y, Liu J, Ma H (2019) Evolution analysis of the fasciclin-like arabinogalactan proteins in plants shows variable fasciclin-AGP domain constitutions. Int J Molec Sci 20:1945. https://doi.org/10.3390/ijms20081945
Hibi T, Kosugi S, Iwai T, Kawata M, Seo S, Mitsuhara I, Ohashi Y (2007) Involvement of EIN3 homologues in basic PR gene expression and flower development in tobacco plants. J Exp Bot 58:3671–3678. https://doi.org/10.1093/jxb/erm216
Higginson T, Li SF, Parish RW (2003) AtMYB103 regulates tapetum and trichome development in Arabidopsis thaliana. Pl J 35:177–192. https://doi.org/10.1046/j.1365-313x.2003.01791.x
Huang GQ, Xu WL, Gong SY, Li B, Wang XL, Xu D, Li XB (2008) Characterization of 19 novel cotton FLA genes and their expression profiling in fiber development and in response to phytohormones and salt stress. Physiol Pl 134:348–359. https://doi.org/10.1111/j.1399-3054.2008.01139.x
Huynh-Thu VA, Irrthum A, Wehenkel L, Geurts P (2010) Inferring regulatory networks from expression data using tree-based methods. PLoS ONE 5:12776. https://doi.org/10.1371/journal.pone.0012776
Jiao H, Liu X, Sun S, Wang P, Qiao X, Li J, Tang C, Wu J, Zhang S, Tao S (2018) The unique evolutionary pattern of the hydroxyproline-rich glycoproteins superfamily in Chinese white pear (Pyrus bretschneideri). BMC Pl Biol 18:36. https://doi.org/10.1186/s12870-018-1252-2
Johnson KL, Jones BJ, Bacic A, Schultz CJ (2003) The fasciclin-like arabinogalactan proteins of Arabidopsis. A multigene family of putative cell adhesion molecules. Pl Physiol 133:1911–1925. https://doi.org/10.1104/pp.103.031237
Johnson KL, Kibble NA, Bacic A, Schultz CJ (2011) A fasciclin-like arabinogalactan-protein (FLA) mutant of Arabidopsis thaliana, fla1, shows defects in shoot regeneration. PLoS ONE 6:e25154. https://doi.org/10.1371/journal.pone.0025154
Jun L, Xiaoming W (2012) Genome-wide identification, classification and expression analysis of genes encoding putative fasciclin-like arabinogalactan proteins in Chinese cabbage (Brassica rapa L.). Molec Biol Reprod 39:10541–10555. https://doi.org/10.1007/s11033-012-1940-1
Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS (2017) ModelFinder: fast model selection for accurate phylogenetic estimates. Nature Meth 14:587–589. https://doi.org/10.1038/nmeth.4285
Kim JE, Kim SJ, Lee BH, Park RW, Kim KS, Kim IS (2000) Identification of motifs for cell adhesion within the repeated domains of transforming growth factor-beta-induced gene, betaig-h3. J Biol Chem 275:30907–30915. https://doi.org/10.1074/jbc.M002752200
Kim D, Langmead B, Salzberg SL (2015) HISAT: a fast spliced aligner with low memory requirements. Nature Meth 12:357–360. https://doi.org/10.1038/nmeth.3317
Li W, Liu B, Yu L, Feng D, Wang H, Wang J (2009) Phylogenetic analysis, structural evolution and functional divergence of the 12-oxo-phytodienoate acid reductase gene family in plants. BMC Evol Biol 9:90. https://doi.org/10.1186/1471-2148-9-90
Li J, Yu M, Geng LL, Zhao J (2010) The fasciclin-like arabinogalactan protein gene, FLA3, is involved in microspore development of Arabidopsis. Pl J 64:482–497. https://doi.org/10.1111/j.1365-313X.2010.04344.x
Liao Y, Smyth GK, Shi W (2014) featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30:923–930. https://doi.org/10.1093/bioinformatics/btt656
Liu F, Xu Y, Jiang H, Jiang C, Du Y, Gong C, Wang W, Zhu S, Han G, Cheng B (2016) Systematic identification, evolution and expression analysis of the Zea mays PHT1 gene family reveals several new members involved in root colonization by arbuscular mycorrhizal fungi. Int J Molec Sci 17:930. https://doi.org/10.3390/ijms17060930
Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(T)(-Delta Delta C) method. Methods 25:402–408. https://doi.org/10.1006/meth.2001.1262
Ma H, Zhao J (2010) Genome-wide identification, classification, and expression analysis of the arabinogalactan protein gene family in rice (Oryza sativa L.). J Exp Bot 61:2647–2668. https://doi.org/10.1093/jxb/erq104
MacMillan CP, Mansfield SD, Stachurski ZH, Evans R, Southerton SG (2010) Fasciclin-like arabinogalactan proteins: specialization for stem biomechanics and cell wall architecture in Arabidopsis and Eucalyptus. Pl J 62:689–703. https://doi.org/10.1111/j.1365-313X.2010.04181.x
MacMillan CP, Taylor L, Bi Y, Southerton SG, Evans R, Spokevicius A (2015) The fasciclin-like arabinogalactan protein family of Eucalyptus grandis contains members that impact wood biology and biomechanics. New Phytol 206:1314–1327. https://doi.org/10.1111/nph.13320
Maere S, Heymans K, Kuiper M (2005) BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics 21:3448–3449. https://doi.org/10.1093/bioinformatics/bti551
Marchler-Bauer A, Derbyshire MK, Gonzales NR, Lu S, Chitsaz F, Geer LY, Geer RC, He J, Gwadz M, Hurwitz DI, Lanczycki CJ, Lu F, Marchler GH, Song JS, Thanki N, Wang Z, Yamashita RA, Zhang D, Zheng C, Bryant SH (2015) CDD: NCBI’s conserved domain database. Nucl Acids Res 43:D222-226. https://doi.org/10.1093/nar/gku1221
Marchler-Bauer A, Bo Y, Han L, He J, Lanczycki CJ, Lu S, Chitsaz F, Derbyshire MK, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Lu F, Marchler GH, Song JS, Thanki N, Wang Z, Yamashita RA, Zhang D, Zheng C, Geer LY, Bryant SH (2017) CDD/SPARCLE: functional classification of proteins via subfamily domain architectures. Nucl Acids Res 45:D200–D203. https://doi.org/10.1093/nar/gkw1129
Meng D, He M, Bai Y, Xu H, Dandekar AM, Fei Z, Cheng L (2018) Decreased sorbitol synthesis leads to abnormal stamen development and reduced pollen tube growth via an MYB transcription factor, MdMYB39L, in apple (Malus domestica). New Phytol 217:641–656. https://doi.org/10.1111/nph.14824
Mizuta Y, Higashiyama T (2014) Antisense gene inhibition by phosphorothioate antisense oligonucleotide in Arabidopsis pollen tubes. Pl J 78:516–526. https://doi.org/10.1111/tpj.12461
Moutinho A, Camacho L, Haley A, Pais MS, Trewavas A, Malhó R (2001) Antisense perturbation of protein function in living pollen tubes. Sexual Pl Reprod 14:101–104. https://doi.org/10.1007/s004970100086
Panchy N, Lehti-Shiu M, Shiu SH (2016) Evolution of gene duplication in plants. Pl Physiol 171:2294–2316. https://doi.org/10.1104/pp.16.00523
Pereira AM, Lopes AL, Coimbra S (2016) Arabinogalactan proteins as interactors along the crosstalk between the pollen tube and the female tissues. Frontiers Pl Sci 7:1895. https://doi.org/10.3389/fpls.2016.01895
Phan HA, Iacuone S, Li SF, Parish RW (2011) The MYB80 transcription factor is required for pollen development and the regulation of tapetal programmed cell death in Arabidopsis thaliana. Pl Cell 23:2209–2224. https://doi.org/10.1105/tpc.110.082651
Preston J, Wheeler J, Heazlewood J, Li SF, Parish RW (2004) AtMYB32 is required for normal pollen development in Arabidopsis thaliana. Pl J 40:979–995. https://doi.org/10.1111/j.1365-313X.2004.02280.x
Qiao X, Li Q, Yin H, Qi K, Li L, Wang R, Zhang S, Paterson AH (2019) Gene duplication and evolution in recurring polyploidization-diploidization cycles in plants. Genome Biol 20:38. https://doi.org/10.1186/s13059-019-1650-2
Ramirez Gonzalez RH, Borrill P, Lang D, Harrington SA, Brinton J, Venturini L, Davey M, Jacobs J, van Ex F, Pasha A, Khedikar Y, Robinson SJ, Cory AT, Florio T, Concia L, Juery C, Schoonbeek H, Steuernagel B, Xiang D, Ridout CJ, Chalhoub B, Mayer KFX, Benhamed M, Latrasse D, Bendahmane A, International Wheat Genome Sequencing C, Wulff BBH, Appels R, Tiwari V, Datla R, Choulet F, Pozniak CJ, Provart NJ, Sharpe AG, Paux E, Spannagl M, Brautigam A, Uauy C (2018) The transcriptional landscape of polyploid wheat. Science 361:6089. https://doi.org/10.1126/science.aar6089
Schultz CJ, Rumsewicz MP, Johnson KL, Jones BJ, Gaspar YM, Bacic A (2002) Using genomic resources to guide research directions. The arabinogalactan protein gene family as a test case. Pl Physiol 129:1448–1463. https://doi.org/10.1104/pp.003459
Sede AR, Wengier DL, Borassi C, Estevez JM, Muschietti JP (2020) Imaging and analysis of the content of callose, pectin, and cellulose in the cell wall of Arabidopsis pollen tubes grown in vitro. Meth Molec Biol 2160:233–242. https://doi.org/10.1007/978-1-0716-0672-8_17
Shi D, Tang C, Wang R, Gu C, Wu X, Hu S, Jiao J, Zhang S (2017) Transcriptome and phytohormone analysis reveals a comprehensive phytohormone and pathogen defence response in pear self-/cross-pollination. Pl Cell Rep 36:1785–1799. https://doi.org/10.1007/s00299-017-2194-0
Showalter AM, Keppler BD, Liu X, Lichtenberg J, Welch LR (2016) Bioinformatic identification and analysis of hydroxyproline-rich glycoproteins in populus trichocarpa. BMC Pl Biol 16:229. https://doi.org/10.1186/s12870-016-0912-3
Steiner-Lange S, Unte US, Eckstein L, Yang C, Wilson ZA, Schmelzer E, Dekker K, Saedler H (2003) Disruption of Arabidopsis thaliana MYB26 results in male sterility due to non-dehiscent anthers. Pl J 34:519–528. https://doi.org/10.1046/j.1365-313x.2003.01745.x
Su S, Higashiyama T (2018) Arabinogalactan proteins and their sugar chains: functions in plant reproduction, research methods, and biosynthesis. Pl Reprod 31:67–75. https://doi.org/10.1007/s00497-018-0329-2
Takahashi D, Kawamura Y, Uemura M (2016) Cold acclimation is accompanied by complex responses of glycosylphosphatidylinositol (GPI)-anchored proteins in Arabidopsis. J Exp Bot 67:5203–5215. https://doi.org/10.1093/jxb/erw279
Trifinopoulos J, Nguyen LT, von Haeseler A, Minh BQ (2016) W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis. Nucl Acids Res 44:W232–W235. https://doi.org/10.1093/nar/gkw256
Wang D, Zhang Y, Zhang Z, Zhu J, Yu J (2010) KaKs_Calculator 2.0: a toolkit incorporating gamma-series methods and sliding window strategies. Genom Proteom Bioinf 8:77–80. https://doi.org/10.1016/S1672-0229(10)60008-3
Wang Y, Wang X, Paterson AH (2012) Genome and gene duplications and gene expression divergence: a view from plants. Ann New York Acad Sci 1256:1–14. https://doi.org/10.1111/j.1749-6632.2011.06384.x
Wang H, Jiang C, Wang C, Yang Y, Yang L, Gao X, Zhang H (2015) Antisense expression of the fasciclin-like arabinogalactan protein FLA6 gene in populus inhibits expression of its homologous genes and alters stem biomechanics and cell wall composition in transgenic trees. J Exp Bot 66:1291–1302. https://doi.org/10.1093/jxb/eru479
Waterhouse AM, Procter JB, Martin DM, Clamp M, Barton GJ (2009) Jalview Version 2–a multiple sequence alignment editor and analysis workbench. Bioinformatics 25:1189–1191. https://doi.org/10.1093/bioinformatics/btp033
Wu J, Wang Z, Shi Z, Zhang S, Ming R, Zhu S, Khan MA, Tao S, Korban SS, Wang H, Chen NJ, Nishio T, Xu X, Cong L, Qi K, Huang X, Wang Y, Zhao X, Wu J, Deng C, Gou C, Zhou W, Yin H, Qin G, Sha Y, Tao Y, Chen H, Yang Y, Song Y, Zhan D, Wang J, Li L, Dai M, Gu C, Wang Y, Shi D, Wang X, Zhang H, Zeng L, Zheng D, Wang C, Chen M, Wang G, Xie L, Sovero V, Sha S, Huang W, Zhang S, Zhang M, Sun J, Xu L, Li Y, Liu X, Li Q, Shen J, Wang J, Paull RE, Bennetzen JL, Wang J, Zhang S (2013) The genome of the pear (Pyrus bretschneideri Rehd.). Genome Res 23:396–408. https://doi.org/10.1101/gr.144311.112
Wu X, Lai Y, Lv L, Ji M, Han K, Yan D, Lu Y, Peng J, Rao S, Yan F, Zheng H, Chen J (2020) Fasciclin-like arabinogalactan gene family in Nicotiana benthamiana: genome-wide identification, classification and expression in response to pathogens. BMC Pl Biol 20:305. https://doi.org/10.1186/s12870-020-02501-5
Xue H, Veit C, Abas L, Tryfona T, Maresch D, Ricardi MM, Estevez JM, Strasser R, Seifert GJ (2017) Arabidopsis thaliana FLA4 functions as a glycan-stabilized soluble factor via its carboxy-proximal Fasciclin 1 domain. Pl J 91:613–630. https://doi.org/10.1111/tpj.13591
Yang Z (2007) PAML 4: phylogenetic analysis by maximum likelihood. Molec Biol Evol 24:1586–1591. https://doi.org/10.1093/molbev/msm088
Zhang Z, Xiao J, Wu J, Zhang H, Liu G, Wang X, Dai L (2012b) ParaAT: a parallel tool for constructing multiple protein-coding DNA alignments. Biochem Biophys Res Commun 419:779–781. https://doi.org/10.1016/j.bbrc.2012.02.101
Zhang H, Gao S, Lercher MJ, Hu S, Chen W-H (2012a) EvolView, an online tool for visualizing, annotating and managing phylogenetic trees. Nucl Acids Res 40:W569–W572. https://doi.org/10.1093/nar/gks576
Zhang Z, Xin W, Wang S, Zhang X, Dai H, Sun R, Frazier T, Zhang B, Wang Q (2015) Xylem sap in cotton contains proteins that contribute to environmental stress response and cell wall development. Funct Integr Genomics 15:17–26. https://doi.org/10.1007/s10142-014-0395-y
Zhou H, Yin H, Chen J, Liu X, Gao Y, Wu J, Zhang S (2016) Gene-expression profile of developing pollen tube of Pyrus bretschneideri. Gene Expr Patterns 20:11–21. https://doi.org/10.1016/j.gep.2015.10.004
Acknowledgements
This work was funded by the National Key Research and Development Program of China (Grant No. 2020YFE0202900), National Natural Science Foundation of China (31772256, 31772276), Fundamental Research Funds for the Central Universities (JCQY201903, KYLH202002), Jiangsu Province Science and Technology Support Program (BE2018389), the Priority Academic Program Development of Jiangsu Higher Education Institutions. Bioinformatic analysis was supported by the Bioinformatics Center of Nanjing Agricultural University. Usage of microscope was guided by Yuehua Ma.
Author information
Authors and Affiliations
Contributions
Peng Wang conceived and designed the experiments, Xiaoqiang Li and Mengyu Cheng performed the experiments, and Xiaoqiang Li wrote the manuscript. The manuscript was revised and confirmed by Chao Tang, Xiaoxuan Zu, Kaijie Qi, Shaoling Zhang and Juyou Wu. All those involved have read and confirmed the paper.
Corresponding author
Ethics declarations
Competing interests
The authors declare that they have no competing interests.
Additional information
Handling editor: Christian Parisod.
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Information
Below is the link to the electronic supplementary material.
Information on Electronic Supplementary Material
Information on Electronic Supplementary Material
Online Resource 1. Multiple sequence alignment of the fasciclin domains of PbrFLAs.
Online Resource 2. RNA-seq data analysis of PbrFLAs in different developmental stages of pear pollen tube and different pollinated style.
Online Resource 3. Co-expression relationships between PbrFLA10/20/21 genes and transcription factor genes.
Online Resource 4. List of genome information of seven Rosaceae species.
Online Resource 5. List of the number of genes of each subfamily in Arabidopsis thaliana and seven Rosaceae species.
Online Resource 6. List of gene features of all identified FLA genes in seven Rosaceae.
Online Resource 7. List of motif sequences identified by MEME tools in pear FLA.
Online Resource 8. List of collibearity relationship and Ka/Ks analysis among FLA genes in the same species.
Online Resource 9. List of orthologous pairs of FLA genes between two Rosaceae species.
Online Resource 10. List of the relative expression levels of PbrFLA genes expression in six tissues.
Online Resource 11. List of the TPM value of PbrFLA genes expression in different development of pollen.
Online Resource 12. List of the TPM value of PbrFLA genes expression in different pollinated style.
Online Resource 13. List of primers for qRT-PCR of PbrFLA candidate genes and atisense oligo deoxynucleotide experiment in pear.
Online Resource 14. List of gene co-expression network analysis of PbrFLA genes in pear.
Rights and permissions
About this article
Cite this article
Li, X., Cheng, M., Tang, C. et al. Identification and function analysis of fasciclin-like arabinogalactan protein family genes in pear (Pyrus bretschneideri). Plant Syst Evol 307, 48 (2021). https://doi.org/10.1007/s00606-021-01769-w
Received:
Accepted:
Published:
DOI: https://doi.org/10.1007/s00606-021-01769-w